Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Common
common (popmax 46.1%, amr) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.63 | GERP 0.78, phastCons 1 |
| Overall | ||
| CADD | 9.264 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
46.1%
Admixed American · 27,683/59,990 alleles
Filtering AF
45.7%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 45.5%
Overall
28.4%
457,697/1,613,714 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 46.1% | 2 |
| East Asian | 38.7% | 3 |
| South Asian | 36.2% | 3 |
| African / African-American | 32.4% | 3 |
| Remaining individualsnot grpmax-eligible | 29.2% | 3 |
| Finnishnot grpmax-eligible | 28.7% | 3 |
| Ashkenazi Jewishnot grpmax-eligible | 27.6% | 4 |
| European (non-Finnish) | 26.2% | 4 |
| Middle Eastern | 24.6% | 4 |
| Amishnot grpmax-eligible | 20.2% | 5 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- DNAH2
- Protein
- p.Pro1384=
- Coding
- c.4152C>G
- MANE Select
- NM_020877
- dbSNP
- rs9909288
- Type
- single nucleotide variant
- Location
- chr17:7770610 (GRCh38)
- Gene constraint
- LOEUF 0.655 · pLI <0.01 (gnomAD)
- Residue 1384
- the 'stem' region
Similar variants
- DNAH2 p.Ala1036Val Uncertain significance ★★ ⚠ same type
- DNAH2 p.Arg1533Cys Uncertain significance ★★ ⚠ same type
- DNAH2 p.Arg2538Gln Uncertain significance ★★ same type
- DNAH2 p.Arg3759His Uncertain significance ★★ ⚠ same type
- DNAH2 p.Gln2069Glu Uncertain significance ★★ same type
- DNAH2 p.Ile4043Ser Uncertain significance ★★ ⚠ same type
- DNAH2 p.Pro3819Leu Uncertain significance ★★ ⚠ same type
- DNAH2 c.10169+3G>A Benign ★★ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/dnah2-p-pro1384 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown